A comparison of automated segmentation and manual tracing for quantifying hippocampal and amygdala volumes

By R. Morey, C. Petty, Yuan Xu, J. Hayes, H. Ryan Wagner II, D. Lewis, Kevin S. LaBar, Martin Andreas Styner, Gregory McCarthy. NeuroImage, 2008

576 citations recorded by the source corpus.

Large databases of high-resolution structural MR images are being assembled to quantitatively examine the relationships between brain anatomy, disease progression, treatment regimens, and genetic influences upon brain structure. Quantifying brain structures in such large databases cannot be practically accomplished by expert neuroanatomists using hand-tracing. Rather, this research will depend upon automated methods that reliably and accurately segment and quantify dozens of brain regions. At present, there is little guidance available to help clinical research groups in choosing such tools. Thus, our goal was to compare the performance of two popular and fully automated tools, FSL/FIRST and FreeSurfer, to expert hand tracing in the measurement of the hippocampus and amygdala. Volumes derived from each automated measurement were compared to hand tracing for percent volume overlap, percent volume difference, across-sample correlation, and 3-D group-level shape analysis. In addition, sample size estimates for conducting between-group studies were computed for a range of effect sizes. Compared to hand tracing, hippocampal measurements with FreeSurfer exhibited greater volume overlap, smaller volume difference, and higher correlation than FIRST, and sample size estimates with FreeSurfer were closer to hand tracing. Amygdala measurement with FreeSurfer was also more highly correlated to hand tracing than FIRST, but exhibited a greater volume difference than FIRST. Both techniques had comparable volume overlap and similar sample size estimates. Compared to hand tracing, a 3-D shape analysis of the hippocampus showed FreeSurfer was more accurate than FIRST, particularly in the head and tail. However, FIRST more accurately represented the amygdala shape than FreeSurfer, which inflated its anterior and posterior surfaces.

Subfields: Cognitive Neuroscience, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/0f2d216d26e47d3bd54b7eee33f59000ee066de9

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Citations in the corpus

Sensitive periods of amygdala development: The role of maltreatment in preadolescence (2014, methodology): “Overall, FreeSurfer provides one of the most reliable automated brain segmentation methods for assessing the amygdala and thesemeasures correlate highlywith expert hand tracings (Morey et al., 2009).”
Patch-based segmentation using expert priors: Application to hippocampus and ventricle segmentation (2011, result): “For HC segmentation, recently published results (Barnes et al., 2008; Chupin et al., 2007; Morey et al., 2009; Morra et al., 2008; Pohl et al., 2007; van der Lijn et al., 2008) indicated high kappa index values greater than 0.80.”
A Bayesian model of shape and appearance for subcortical brain segmentation (2011, unknown): “…al. (2010); Cherubini et al. (2010); Gholipour et al. (2009); Luo et al. (2009); Sotiropoulos et al. (2010); Erickson et al. (2009); Péran et al. (2009); Erickson et al. (2010a,b); Filippini et al. (2009); Janssen et al. (2009); Chan et al. (2009); Babalola et al. (2007); Morey et al. (2009, 2010).”
Behavior Problems After Early Life Stress: Contributions of the Hippocampus and Amygdala (2014, background): “Methods such as FreeSurfer yield high variability and low validity for regions such as the amygdala (67,68), often changing study results (Supplement 1) (69).”
The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements (2012, background): “[4]: the percentage absolute volume differences with respect to manual were about 4.”
The influence of puberty on subcortical brain development (2014, background): “…reported volume increases with increasing pubertal stage (and testosterone level) in males (Bramen et al., 2011; Neufang et al., 2009), but have had conflicting results in females, where both increases (Neufang et al., 2009) and decreases (Bramen et al., 2011) in amygdala volume have been reported.”